RetrogeneDB ID: | retro_cjac_3858 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285215.1:14139..15897(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NOD2 | ||
| Ensembl ID: | ENSCJAG00000001786 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3858
CAGTCCCCGTTCCTCAGGAAGTCAGGAAGGGGCAGAGACGCTTTGCCTGGAGGACATATACCCAGAGAATGTCCTGGAGG
TCTGGGCAGATATGGGCATGGCTGGATCCCTGCAGAAGAGCCCGGACACCCTGGGGCTGGAGGAGCTCTTCAGCACCCTT
GGCCACCTCAGTGAAGATGTGCTGGTGGGGGGTGAGGCAGGCAGTGGCAAGAGCATGCTCCTGCAGCGTCTGCACTTGCC
GTGGGCTGCAGGGCGAGACTTCCAGGAATTTTTCTTTGTCTTCCCATTCAGCTGCCGGCAGCTGCAGTGAATGGTTAAAC
CACTCTCTGTGCGGATGCTACTCTTTGAGCACTGCTGTTGGCCTGACCTTGATCAACAGGACATCTTCCAGTTTCTCCTT
GACCACCCTGACCGTGTCCGGCTAACCTTTGATGGCTTTGATGAGTTCAAGTTCAGGTTCACGGATTGCGAATGTCACTG
CTCCCTGACAGACCCCACCTCTGTCCAGACTCTGCTCTTTAACCTTCTGCAGGTCAACCTGCTGAAGAATGCCCGCAAGG
TGGTGACCAGCCGTCCTGCTTCCGTGTCGGCGTTCCTCAGGAAGTACATCTGCACCGAGTTCATCCTCAAGGGCTTCTCC
GAAGAGGGCATCGAGCTGTACTTGAGGAAGCGCCATCATGATCCTGGAGTGGCAGACCGCCTCATTCGCCTGCTCCAAGC
GTCCTCAGCCCTGAGTGGTTTGTGCCACCTTCCTGTGTTCTCATGGATGGTGTCCAAATGCCACCAGGAACTGTTGCTGC
AGAGGGCGGGGGGGATCCCCAAAGACCACTACAGATATGTACCTGCTGATCCTGCAGCATTTTCTGCTGCATGCCATCCC
CCCAGACTCAGCCTGCCAGGGTCTAGGACCCAGTCTCCTTCTGGGCCACCTCCCCACCCTCCTGTGCCTCGGCAGACTTG
CTCTCTGGGCCTGGGCATGTGCTGCTATGTGTTCTCAGCCCAGCAGCTCCAGGCAGCACAGGTCAGTCCTGATGACATTT
CTCTTGGCTTCCTGGTATGTGCCAAAGGTGTCATGCCAGAGAGTACAGTGCCCCTGGAATTCCTGCACATCACTTTCCAG
TGCTTCTTTGCCGTGTTCTACCTGGCACTCAGTGCTGATGTGCCGCCAGCCTTGATCAGGCACCTCTTCAGTTGTGGCAG
GCCAGGCAACTCGCTGATGGCCAGGCTCCTGCCCATGCTGTGCATCCAGGGCTTGCAGGGGAAGGACGGCAGTGTGGCAG
CTTTGCTGCAGAAGACTGAGCTGCACAGCCTTTAGATCACAGCAGCCTTCCTGGCAGGGCTGTTGTCCTGAGAGCACTGG
GGCCTGCTGGCCGAGTGCCAGGCATCCGAGAAGGCCCTGCTCCGGCGCCAGGTCTGTGCCCGCTAGTGTCTGGCCCGCAG
CCTCTGTAAGCACTTCCACTCCATCCTGCCAGCCGTGCCAGGTGAGGCCAAGAGCATGCACGCCATGTCCAGGTTCATCT
GGCTCATACAGAGCCTGTACGAGATGCAAATGAGCAGCTGGCATGGAAGGCTGTACGTGGCCTGAATGTCGGGCACCTCA
AGTTGACATTTTGCAGCATGGGCCCCACTGAGTGTGCTGCCCTGGCCTTCGTGTGGTGGCACCTCCAGCAGCCCGTGGCC
CTGCAGTTGGACTACAACTCTGTGGGTGACATTGATGTGGAGCAGCTTCTGCCTTGCCTTGGTGTCTGCAAGGCTCTG
ORF - retro_cjac_3858 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.38 % |
| Parental protein coverage: | 72.66 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | QSRFL-STYDGAETLCLEDIYTENVLEVWADVGVAGLPQKSPATLGLEELFSTPGHLSDDADTVLVVGEA |
| QS.FL.....GAETLCLEDIY.ENVLEVWAD.G.AG..QKSP.TLGLEELFST.GHLS.D...VLV.GEA | |
| Retrocopy | QSPFL>GSQEGAETLCLEDIYPENVLEVWADMGMAGSLQKSPDTLGLEELFSTLGHLSED---VLVGGEA |
| Parental | GSGKSTLLQRLHLLWAAGRDFQEFLFVFPFSCRQLQCVVKPLSVQMLLFEHCCWPDVDQQDIFQFLLDHP |
| GSGKS.LLQRLHL.WAAGRDFQEF.FVFPFSCRQLQ..VKPLSV.MLLFEHCCWPD.DQQDIFQFLLDHP | |
| Retrocopy | GSGKSMLLQRLHLPWAAGRDFQEFFFVFPFSCRQLQ*MVKPLSVRMLLFEHCCWPDLDQQDIFQFLLDHP |
| Parental | DRVLLTFDGFDEFKFRFSDRERHCSPTDPTSVQTLLFNLLQVNLLKNARKVVTSRPASMSAFLRKYIHTE |
| DRV.LTFDGFDEFKFRF.D.E.HCS.TDPTSVQTLLFNLLQVNLLKNARKVVTSRPAS.SAFLRKYI.TE | |
| Retrocopy | DRVRLTFDGFDEFKFRFTDCECHCSLTDPTSVQTLLFNLLQVNLLKNARKVVTSRPASVSAFLRKYICTE |
| Parental | FILKGFSKEGIELYLRKRHHDPGVADRLIRLLQASSALSGLCHLPVFSWMVSKCHQELMLLQR-RGGSPK |
| FILKGFS.EGIELYLRKRHHDPGVADRLIRLLQASSALSGLCHLPVFSWMVSKCHQEL.LLQR.RGGSPK | |
| Retrocopy | FILKGFSEEGIELYLRKRHHDPGVADRLIRLLQASSALSGLCHLPVFSWMVSKCHQEL-LLQR>RGGSPK |
| Parental | TTTDMYLLILQHFLLHAIPPDSACHILGPSLLLGCLPTLLRLGRLALW-GLGMCCYVFSAQQLQAAQVSP |
| TTTDMYLLILQHFLLHAIPPDSAC..LGPSLLLG.LPTLL.LGRLALW.GLGMCCYVFSAQQLQAAQVSP | |
| Retrocopy | TTTDMYLLILQHFLLHAIPPDSACQGLGPSLLLGHLPTLLCLGRLALW<GLGMCCYVFSAQQLQAAQVSP |
| Parental | DDISLGFLVCAKGVMPESTVPLEFLHITFQCFFAAFYLALSADVPPALLRHLFNCGRPGNSPMARLLPML |
| DDISLGFLVCAKGVMPESTVPLEFLHITFQCFFA.FYLALSADVPPAL.RHLF.CGRPGNS.MARLLPML | |
| Retrocopy | DDISLGFLVCAKGVMPESTVPLEFLHITFQCFFAVFYLALSADVPPALIRHLFSCGRPGNSLMARLLPML |
| Parental | CIQGSRGKDGSVAALLQKTEPHNLQITAAFLAGLLSWEHWGLLAECQASKKALLQRQACARWCLARSLRK |
| CIQG..GKDGSVAALLQKTE.H.L.ITAAFLAGLLS.EHWGLLAECQAS.KALL.RQ.CAR.CLARSL.K | |
| Retrocopy | CIQGLQGKDGSVAALLQKTELHSL*ITAAFLAGLLS*EHWGLLAECQASEKALLRRQVCAR*CLARSLCK |
| Parental | HFHSIPPAAPGEAKSMHAMPRFIWLLRSLYEMQ-DERLARKAVRGLNVGHLKLTFCSVGPTECAALAFVL |
| HFHSI.PA.PGEAKSMHAM.RFIWL..SLYEMQ..E.LA.KAVRGLNVGHLKLTFCS.GPTECAALAFV. | |
| Retrocopy | HFHSILPAVPGEAKSMHAMSRFIWLIQSLYEMQ<NEQLAWKAVRGLNVGHLKLTFCSMGPTECAALAFVW |
| Parental | RHLQRPVALQLDYNSVGDIGVEQLLPCLGVCKAL |
| .HLQ.PVALQLDYNSVGDI.VEQLLPCLGVCKAL | |
| Retrocopy | WHLQQPVALQLDYNSVGDIDVEQLLPCLGVCKAL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .13 RPM | 1 .15 RPM |
| SRP051959_heart | 0 .18 RPM | 2 .32 RPM |
| SRP051959_kidney | 0 .07 RPM | 0 .98 RPM |
| SRP051959_liver | 0 .09 RPM | 2 .36 RPM |
| SRP051959_lung | 0 .26 RPM | 2 .28 RPM |
| SRP051959_lymph_node | 0 .16 RPM | 2 .03 RPM |
| SRP051959_skeletal_muscle | 0 .59 RPM | 11 .36 RPM |
| SRP051959_spleen | 0 .08 RPM | 2 .21 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3858 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3858 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3858 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001786 | 1 retrocopy |
retro_cjac_3858 ,
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